Hi All, I’ve recently made the mistake of updating to MacOS26 before checking to see if old COOT will be affected. This is now the case and I can’t use old COOT on MacOS26.
I have used COOT 1 some times too but I have recently had an issue that causes it to crash and in the terminal I get a segmentation fault error. I noticed this happened after I manually edited a PDB file while it was loaded and active in COOT 1. When I now try and launch COOT 1, I think it tries to load the previous file with the ligand for some reason as some sort of backup but the file no longer contains the coordinates for this ligand and then the segmentation fault happens. I’ve tried uninstalling the whole CCP4 package and COOT files I could find on my MAC and then reinstalling everything but COOT 1 still crashes with the same segmentation fault trying to look up some previous structures I worked on. Is there some hidden cache file for COOT 1 that I can delete so that it longer goes looking for previous structures I worked on? Below I’ve added the segmentation fault string, I can’t add more details due to target info I’m working on. WARNING:: no molecule for imol = 0 WARNING:: atom with name " CA" alt-loc "empty", res-no: 252, ins-code "", chain: "B" not found in molecule 0 /Applications/ccp4-9/coot_py3/bin/coot: line 209: 15158 Segmentation fault: 11 $coot_bin "$@" Coot crashed. Many Regards, Chris Browning -- Dr. Christopher Browning Principal Research Scientist Vertex Pharmaceuticals 86-88 Jubilee Avenue Milton Park Abingdon OX14 4RW UK From: CCP4 bulletin board <[email protected]> on behalf of Paul Emsley <[email protected]> Date: Monday, 24 November 2025 at 20:40 To: [email protected] <[email protected]> Subject: Re: [ccp4bb] Coot/ccp4/pymol/phenix/Relion/etc and MacOS26? CAUTION: This email originated from outside of Vertex. Do not open links or attachments unless you know the sender and believe it is safe. If you suspect that this email is a potentially malicious email, please click on the Report Phish button. On 24/11/2025 09:03, Henry Man wrote: > I have recently updated to MacOS 26.1, I can highly recommend that you do not > for now. > It has broken something with X11/XQuartz and therefore coot (0.9.8.96) is no > longer launching. > Others have bought up this issue with XQuartz github > (https://urldefense.com/v3/__https://github.com/XQuartz/XQuartz/issues/438__;!!FRfS_D4!Yio4zVGkNDYHti6bbG0zDDok530BkMb7QEdIIrkzYmHDUnb6xcZIcZCfd1mkRB99mVi3WT4F7G9OhUX289tWcApwp49anmbXlqRq1l40_Zrd$ > ). > > If anyone has any work arounds or fixes, would be very helpful to a coot-less > crystallographer. Why are you Coot-less? CCP4 distributes a quite recent version of Coot 1, as does homebrew. Paul. ######################################################################## To unsubscribe from the CCP4BB list, click the following link: https://urldefense.com/v3/__https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1__;!!FRfS_D4!Yio4zVGkNDYHti6bbG0zDDok530BkMb7QEdIIrkzYmHDUnb6xcZIcZCfd1mkRB99mVi3WT4F7G9OhUX289tWcApwp49anmbXlqRq1kwDfk8V$ This message was issued to members of https://urldefense.com/v3/__http://www.jiscmail.ac.uk/CCP4BB__;!!FRfS_D4!Yio4zVGkNDYHti6bbG0zDDok530BkMb7QEdIIrkzYmHDUnb6xcZIcZCfd1mkRB99mVi3WT4F7G9OhUX289tWcApwp49anmbXlqRq1t_PZwu-$ , a mailing list hosted by https://urldefense.com/v3/__http://www.jiscmail.ac.uk__;!!FRfS_D4!Yio4zVGkNDYHti6bbG0zDDok530BkMb7QEdIIrkzYmHDUnb6xcZIcZCfd1mkRB99mVi3WT4F7G9OhUX289tWcApwp49anmbXlqRq1iSlDyOv$ , terms & conditions are available at https://urldefense.com/v3/__https://www.jiscmail.ac.uk/policyandsecurity/__;!!FRfS_D4!Yio4zVGkNDYHti6bbG0zDDok530BkMb7QEdIIrkzYmHDUnb6xcZIcZCfd1mkRB99mVi3WT4F7G9OhUX289tWcApwp49anmbXlqRq1ni1CF4a$ This email message and any attachments are confidential and intended for use by the addressee(s) only. If you are not the intended recipient, please notify me immediately by replying to this message, and destroy all copies of this message and any attachments. Thank you. For information on how Vertex processes personal data, please see our Global Privacy Notice<https://www.vrtx.com/international-privacy/> ######################################################################## To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
